How to make changes to my vertex groups with python
Ultimately what was missing here was another look at the core issue. Only toggling a suffix on and off was not the answer. My groups had names that differed by one character to their counterpart and regardless of having the correct .L/.R suffix, meant they could not link with the mirror modifier. I did not need to delete the vertex groups relevant to the mesh side I had deleted as previously thought.

That being said, this is the code you're after if you need to achieve something similar.

In my case, remove the prefix that caused the group names to no longer be linked to their counterparts [4:]. Add the correct suffixes. Revert both of these changes when the script is run again for import back to game.

import bpy
active_object = bpy.context.active_object

vertex_groups = active_object.vertex_groups[:]

for vertex_group in vertex_groups:
    if vertex_group.name.endswith('.L'):
        vertex_group.name = 'b__L' + vertex_group.name.replace('.L', '')
        continue
    if vertex_group.name.endswith('.R'):
        vertex_group.name = 'b__R' + vertex_group.name.replace('.R', '')
        continue
    if (vertex_group.name.startswith('b__L') | vertex_group.name.startswith('b__R')):
        suffix = '.L' if vertex_group.name.startswith('b__L') else '.R'
        vertex_group.name = vertex_group.name[4:] + suffix


Thanks to my lovely sister for this script. Hope it can help someone else out there!